Not bothering to sleep, eat, drink, or get out of my chair for an entire weekend until I had finished the game in one sitting is my strongest memory of Star Control. Second would be the Orz, and having to learn their "Language". The word "Dance" has been synonymous with "fight" for me ever since.
Oh, and changing the Ilwrath word for "warship" to "worship", for some reason that always stuck in my mind as being really cool.